Category Archives: Animal microbiome

March 13, 2016

Posted on by

General microbiome

Review: Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications – S. Woloszynek – International Review of Cell and Molecular Biology

Pregnancy and birth / Human vaginal microbiome

Review: The vaginal microbiota, host defense and reproductive physiology – Steven B Smith – The Journal of Physiology

Human gut microbiome

Review: Brain-Gut-Microbiota axis: Challenges for Translation in Psychiatry – John R. Kelly – Annals of Epidemiology

Editorial: The microbiome in celiac disease: Beyond diet-genetic interactions – Jose U. Scher – Cleveland Clinic Journal of Medicine
Animal models

Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model – Gaorui Bian – Environmental Microbiology

Heat-treated high-fat diet modifies gut microbiota and metabolic markers in apoe−/− mice – Nittaya Marungruang – Nutrition & Metabolism

Animal microbiome

Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee – Quinn S. McFrederick – Molecular Ecology

Plant, root, and soil microbiome

Cry1Ac Transgenic Sugarcane Does Not Affect the Diversity of Microbial Communities and Has No Significant Effect on Enzyme Activities in Rhizosphere Soil within One Crop Season – Dinggang Zhou – Frontiers in Plant Science

Succession of soil microbial communities and enzyme activities in artificial soils – Franziska Ditteric – Pedobiologia

Effect of copper and zinc on microbial tolerance to triclosan in two soil types – Gerty J. H. P. Gielen – Journal of Soils and Sediments

Microbial enzymes as an early warning management tool for monitoring mining site soils – Mohammad Wahsha – CATENA

Water and glacier microbiome

Bacterial communities potentially involved in iron-cycling in Baltic Sea and North Sea sediments revealed by pyrosequencing – Carolina Reyes – FEMS Microbiology Ecology

The Differing Biogeochemical and Microbial Signatures of Glaciers and Rock Glaciers – Timothy S. Fegel – Journal of Geophysical Research

Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon – Florent E. Angly – PeerJ

Infection microbiology

Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans – Salah Zangena – Scientific Reports

Viruses

RNA viruses as major contributors to Antarctic virioplankton – Jaclyn A Miranda – Environmental Microbiology

Review: Giant viruses of amoebas: an update – Sarah Aherfi – Frontiers in Microbiology

Microbial Ecology

Review: Dancing with the Stars: How Choreographed Bacterial Interactions Dictate Nososymbiocity and Give Rise to Keystone Pathogens, Accessory Pathogens, and Pathobionts – George Hajishengallis – Trends in Microbiology

Metagenomics and bioinformatics

LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly – Paola Bonizzoni – Journal of Computational Biology

Microbes in the news

Cool Citizen Microbiology Project in Spain With Great Engagement – David Coil – Microbenet

Podcast: The Bacteria Behind Your Favorite Blues, Bries, and More – Science Friday

Science, publishing and career

Scientists who tweet: 3 Fred Hutch researchers talk about getting #science out into the world, 140 characters at a time – Mary Engel – Fred Hutch

This Student Adds A Woman In Science To Wikipedia Every Time She’s Harassed Online – Kelly Oakes – BuzzFeed

Bik’s Picks

Neandertals’ large lower thorax may represent adaptation to high protein diet – Miki Ben-Dor – American Journal of Physical Anthropology

[hr]

March 12, 2016

Posted on by

Microbiomes of farmland frogs and grape vine, and functional structures in acid mine drainage microbes.

Human oral microbiome

Ecological changes in oral microcosm biofilm during maturation – Young-Seok Kim – Journal of Biomedical Optics

Human gut microbiome

Review: Consequences of bile salt biotransformations by intestinal bacteria – Jason M. Ridlon – Gut Micobes

Review: The microbiota–gut–brain axis and its potential therapeutic role in autism spectrum disorder – Q. Li,- Neuroscience

Animal models

Safety Evaluation of Neo Transgenic Pigs by Studying Changes in Gut Microbiota Using High-Throughput Sequencing Technology – Qingqing Wang – PLOS ONE

Animal microbiome

Changes of diet and dominant intestinal microbes in farmland frogs – Chun-Wen Chang – BMC Microbiology

Plant, soil, and microbiome

Vitis vinifera microbiome: from basic research to technological development – Cátia Pinto – BioControl

Water and extremophile microbiology

Predicting taxonomic and functional structure of microbial communities in acid mine drainage – Jialiang Kuang – The ISME Journal

Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences – Martin W Hahn – The ISME Journal

Waste and pollution microbiology

Changes of microbial composition during wastewater reclamation and distribution systems revealed by high-throughput sequencing analyses – Yiwen Lin – Frontiers of Environmental Science & Engineering

Metabolomics

Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease – Qiang Feng – Scientific Reports

Bioinformatics and metagenomics

Phylogeny-aware Identification and Correction of Taxonomically Mislabeled Sequences – Alexey M Kozlov – BioRxiv

Microbial Ecology

Challenges in microbial ecology: building predictive understanding of community function and dynamics – Widder, S – White Rose Research Online

Microbes in the news

A cloud of distinction – Could the trails of microbes we leave behind be used to solve crimes? Julian Smith picks up the scent – Julian Smith  – New Scientist

Stick Out Your Tongue: Citizen science project draws up the first oral microbiome map for the youth: Over 4,000 people have taken part in this hands-on scientific project in Barcelona- EurekAlert

Biologicals in quest for 2050: BioConsortia is evaluating microbes that could help protect seedlings emerging in cold and wet conditions. – AgriView

Gut Microbiome Analysis for Detecting Colon Cancer Mutations – Univesrity of Minnesota

[hr]

March 11, 2016

Posted on by

Posting from the airport – flying home to my folks for a week. I will try to keep you all updated, though! Fecal microbiota from dolphins (by another group!), microbes and Alzheimer’s, plastic-eating bacteria, and lead exposure.

Pregnancy and birth

State Scope of Practice Laws, Nurse-Midwifery Workforce, and Childbirth Procedures and Outcomes – Y. Tony Yang – Women’s Health Issues

Human oral microbiome

Characterization of a highly arginolytic Streptococcus species that potently antagonizes Streptococcus mutans – Xuelian Huang – Applied and Environmental Microbiology

The Microbiome of the Oral Mucosa in Irritable Bowel Syndrome – Nicolaas H. Fourie – Gut Microbes

Preliminary analysis of salivary microbiome and their potential roles in oral lichen planus
Kun Wang – Scientific Reports

Human respiratory microbiome

Review: The lung microbiome and exacerbations of COPD – Dy, Rajany – Current Opinion in Pulmonary Medicine

Human vaginal microbiome

Unique Insights in the Cervicovaginal Lactobacillus iners and L. crispatus Proteomes and Their Associations with Microbiota Dysbiosis – Hanneke Borgdorff – PLOS ONE

Human gut microbiome

The Microbiome, Intestinal Function, and Arginine Metabolism of Healthy Indian Women Are Different from Those of American and Jamaican Women – CC Kao – Journal of Nutrition

Fecal Microbiota Transplantation Inhibits Multidrug-Resistant Gut Pathogens: Preliminary Report Performed in an Immunocompromised Host – Jarosław Biliński – Archivum Immunologiae et Therapiae Experimentalis

The Intersection of TNF, IBD and the Microbiome – Yava L. Jones-Hall – Gut Microbes

Review: Bacterial species involved in the conversion of dietary flavonoids in the human gut – Annett Braune – Gut Microbes

Review: Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism – Douglas J. Morrison – Gut Microbes

Microbiome models

Perinatal lead (Pb) exposure alters gut microbiota composition and results in sex-specific bodyweight increases in adult mice – Jianfeng Wu – Toxicological Sciences

Castration influences intestinal microflora and induces abdominal obesity in high-fat diet-fed mice – Naoki Harada – Scientific Reports

Animal microbiome

The bottlenose dolphin (Tursiops truncatus) fecal microbiota – Matteo Soverini – FEMS Microbiology Ecology

Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes – Moritz Buck – Scientific Reports

Resistance to antimicrobial agents among enterococci isolated from fecal samples of wild marine species in the southern coast of Brazil – Janira Prichula – Marine Pollution Bulletin

Targeting eukaryote mitochondrial 16S rRNA gene: Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing – Kyle Logue – PLOS Neglected Tropical Diseases

Characterization of caecum and crop microbiota of Indian indigenous chicken targeting multiple hypervariable regions within 16s rRNA gene – S. Saxena – British Poultry Science

Plant, root, and soil microbiome

Nitrogen-fixing bacterial communities in invasive legume nodules and associated soils are similar across introduced and native range populations in Australia – Christina Birnbaum – Journal of Biogeography

Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors? – José A. Siles – Microbial Ecology

Interactions between Bacteria And Aspen Defense Chemicals at the Phyllosphere – Herbivore Interface – Charles J. Mason – Journal of Chemical Ecology

Long-term effects of multi-walled carbon nanotubes and graphene on microbial communities in dry soil – Yuan Ge – Environmental Science and Technology

Air and space station microbiome

Airborne Bacterial Diversity from the Low Atmosphere of Greater Mexico City – Jaime García-Mena – Environmental Microbiology

Characterization of Fungi Isolated from the Equipment Used in the International Space Station or Space Shuttle – Kazuo Satoh – Microbiology and Immunology

Water, waste, and pollution microbiology

A bacterium that degrades and assimilates poly(ethylene terephthalate) – Shosuke Yoshida – Science

The occurrence of PAHs and faecal sterols in Dublin Bay and their influence on sedimentary microbial communities – Brian T. Murphy – Marine Pollution Bulletin

Bacterial communities potentially involved in iron-cycling in Baltic Sea and North Sea sediments revealed by pyrosequencing – Carolina Reyes – Microbiology Ecology

Microbial Ecology

Phylogenetic organization of bacterial activity – Ember M Morrissey – The ISME Journal

Infection and microbiology

Editorial: Microbes and Alzheimer’s Disease – Ruth F. Itzhaki – Journal of Alzheimer’s Disease

Treatment of in vitro enterohemorrhagic E. coli infection using phage and probiotics – Cecilia Dini _ Journal of Applied Microbiology

Microbes in the news

These plastic-eating bacteria could help cut down on waste – Rachel Feltman – Washington Post

Some bacteria think plastic is fantastic – Nicholas S. Wigginton – Science

Science: Newly Identified Bacteria Break Down Tough Plastic – Michelle Hampson – AAAS News

Scientists identify a virus and two bacteria that could be causing Alzheimer’s – Fiona MacDonald – Science Alert

Lead exposure changes gut microbiota, increases chance for obesity – Laurel Thomas Gnagey – University of Michigan

These newly discovered bacteria can help prevent cavities, and scientists want to put them in a pill – Peter Dockrill – Science Alert

Viral infections may affect respiratory microbiome of patients with CF – Healio

Emollient Treatment Improves Skin Microbiome in Atopic Dermatitis: Interview with Sophie Seite – Medical Research

Science, publishing, and career

The Frequency of “Brilliant” and “Genius” in Teaching Evaluations Predicts the Representation of Women and African Americans across Fields – Daniel Storage – PLOS ONE

Papers with simpler abstracts are cited more, study suggests – Dalmeet Singh Chawla – Retraction Watch
[hr]

March 10, 2016

Posted on by

Signals within microbial communities, feeding the microbiome with milk, gut metagenomes of Japanese subjects, multiethnic cohorts, biogeography of viruses in the sea, and finding transcription start sites.

General human microbiome

Review: Signaling in Host-Associated Microbial Communities – Michael A. Fischbach and Julia A. Segre – Cell

Review: The microbiome systemic diseases connection – T.A. van der Meulen – Oral Diseases

Review: The human microbiota: novel targets for hospital-acquired infections and antibiotic resistance – Melinda M. Pettigrew – Annals of Epidemiology

Pregnancy and birth

The placental microbiome is altered among subjects with spontaneous preterm birth with and without chorioamnionitis – Amanda L. Prince – American Journal of Obstetrics and Gynecology

It’s in the Milk: Feeding the Microbiome to Promote Infant Growth – Stavros Bashiardes – Cell Metabolism

The Microbiome in Necrotizing Enterocolitis: A Case Report in Twins and Minireview –
Suchitra K. Hourigan – Clinical Therapeutics

Comment: Gut microbiome and necrotising enterocolitis: time for intervention? –
Alessio Fasano – The Lancet

Human oral microbiome

Not sure if I agree with the goal of this paper: Natural Antimicrobials and Oral Microorganisms: A Systematic Review on Herbal Interventions for the Eradication of Multispecies Oral Biofilms – Lamprini Karygianni – Frontiers in Microbiology

Human urinary tract microbiome

The Urinary Microbiome Differs Significantly between Patients with Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls as Well as between Patients with Different Clinical Phenotypes – Daniel A Shoskes – Urology

Human gut microbiome

The gut microbiome of healthy Japanese and its microbial and functional uniqueness – Suguru Nishijima – DNA Research

Microbiome Heterogeneity Characterizing Intestinal Tissue and Inflammatory Bowel Disease Phenotype – Tyler, Andrea D. – Inflammatory Bowel Diseases

Perspective: Characterisation and therapeutic manipulation of the gut microbiome in inflammatory bowel disease – J. Schulberg – Internal Medicine Journal

FMT Happens: Regulating Fecal Microbiota Therapy in Canada; What You Need to Know – Shahad Salman – World Medical & Health Policy

Review: Characterization of the Gut Microbiome in Epidemiologic Studies: The Multiethnic Cohort Experience – Benjamin C. Fu – Annals of Epidemiology

Review: Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances – M. P. Francino – Frontiers in Microbiology

Animal models

Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes – Chenhong Zhang – ISME Journal

Review: Viruses in Rodent Colonies: Lessons Learned from Murine Noroviruses – Stephanie M. Karst – Annual Review of Virology

Animal microbiome

Study of the Aminoglycoside Subsistence Phenotype of Bacteria Residing in the Gut of Humans and Zoo Animals – Teresita de J. Bello González – Frontiers in Microbiology

Allows the consumption of toxic cabbage: SaxA-mediated isothiocyanate metabolism in phytopathogenic Pectobacteria – Cornelia U. Welte – Applied and Environmental Microbiology

Comparison of Fecal Microbiota of Mongolian and Thoroughbred Horses by High-Throughput Sequencing of the V4 Region of the 16S rRNA Gen (sic) – Yiping Zhao – Asian Australian Journal of Animal Sciences

Potential bacterial core species associated with digital dermatitis in cattle herds identified by molecular profiling of interdigital skin samples – Martin W. Nielsen – Veterinary Microbiology

I really feel for horses who are sick of grass.  Abstract: Analysis of the large intestinal and faecal microbiota of horses with grass sickness using denaturing gradient gel electrophoresis – D. Nölkes – Journal of Equine Veterinary Science

Plant, root, and soil microbiome

Phyllosphere Fungal Communities Differentiate More Thoroughly than Bacterial Communities Along an Elevation Gradient – Corinne Vacher – Microbial Ecology

A compositional shift in the soil microbiome induced by tetracycline, sulfamonomethoxine and ciprofloxacin entering a plant-soil system – Hui Lin – Environmental Pollution

Water and extremophile microbiome

Long-term warming alters richness and composition of taxonomic and functional groups of arctic fungi – József Geml – FEMS Microbiology Ecology

Review: Biogeography of Viruses in the Sea – Cheryl-Emiliane T. Chow – Annual Review of Virology

DGGE: Oil removal and effects of spilled oil on active microbial communities in close to salt‑saturation brines – Yannick Y. Corsellis – Extremophiles

Bioreactors and waste microbiology

Longitudinal Analysis of Microbiota in Microalga Nannochloropsis salina Cultures – Haifeng Geng – Microbial Ecology

Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters – Arda Gülay – ISME Journal

Bacterial communities in different locations, seasons and segments of a dairy wastewater treatment system consisting of six segments – Kikue Hirota – Journal of Environmental Sciences

Food microbiology

Resistome diversity in cattle and the environment decreases during beef production – Noelle R Noyes – eLIFE

Inactivation of Salmonella on tainted foods: using blue light to disinfect cucumbers and processed meat products – J. Stephen Guffey – Food Science & Nutrition

Bioinformatics and metagenomics

Review: Recovering complete and draft population genomes from metagenome datasets – Naseer Sangwan – Microbiome

Dissecting phylogenetic fuzzy weighting: theory and application in metacommunity phylogenetics – Leandro D. S. Duarte – Methods in Ecology and Evolution

Transcriptomics

A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome – Laurence Ettwiller – BMC Genomics

Fungi

Perspective: The invisible dimension of fungal diversity – David Hibbett – Science

Microbes in the news

At Stanford: Center launched to explore, exploit human microbiome – Bruce Goldman – Stanford Medicine

Columbia Expands Its Microbiome Research – Christopher Williams – Columbia University Medical Center

UT professor develops technique to enhance desirable traits of plants, animals through microbiology – Maluly Martinez Benavides – The Daily Texan

5th World Summit “Gut Microbiota For Health”: Media Information on Top Issues Ready for Download

Gut bacteria make cabbage poison harmless – Radboud University

Scientists developed a robust method for analysis of intestinal bacteria – Science Codex

Nukadoko: rich in beneficial bacteria: Nukadoko is made by fermenting rice bran, a byproduct of milling brown rice, with lactic acid bacteria and yeast. – Natsuko Tamaki – The Japan News

A mouse’s house may ruin experiments. Environmental factors lie behind many irreproducible rodent experiments – Sara Reardon – Nature

Viral infections may affect respiratory microbiome of patients with CF – Healio

Science, publishing, and career

German Defense Minister to keep doctoral degree – plagiarism found on 44% – Debora Weber-Wulff – Copy, Shake, and Paste

Bik’s Picks

How long can you chew on goat meat? Impact of meat and Lower Palaeolithic food processing techniques on chewing in humans – Katherine D. Zink – Nature

[hr]

March 9, 2016

Posted on by

Two papers on altered microbiome in HIV-infected humans and SIV-infected monkeys, ESBL carriage in hospital wards and medical students, fungus infection affects frog song, and protein recycling in the ocean.

Pregnancy and birth

Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study – Barbara B Warner – The Lancet

Human gut microbiome

Editorial: The HIV-Associated Enteric Microbiome Has Gone Viral – Brent E. Palmer – Cell Host & Microbe

Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome – Cynthia L. Monaco – Cell Host & Microbe

Comparison of the faecal colonization rates with extended-spectrum beta-lactamase producing enterobacteria among patients in different wards, outpatients and screened medical students – Fatemeh Ebrahimi – Microbiology and Immunology

Animal models

SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination – Scott A. Handley – Cell Host & Microbe

Animal microbiome

Enhanced call effort in Japanese tree frogs infected by amphibian chytrid fungus –
Deuknam An – Biology Letters

Plant, root, and soil microbiome

Diversity and bioactivity of bacterial endophyte community of Cupressaceae – J. Soltani – Forest Pathology

Leaf litter decomposition in remote oceanic island streams is driven by microbes and depends on litter quality and environmental conditions – Verónica Ferreira – Freshwater Biology

Network modules and hubs in plant-root fungal biomes – Hirokazu Toju – Journal of the Royal Society Interface

Water and extremophile microbiome

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean – William D Orsi – The ISME Journal

Food microbiology

Detection of pathogenic Escherichia coli and microbiological quality of chilled shrimp sold in street markets – Liliana Jose Barbosa – Letters in Applied Microbiology

More microbiology

Antimicrobial activity of extracts from macroalgae Ulva lactuca against clinically-important Staphylococci is impacted by lunar phase of macroalgae harvest – Amy M. Deveau – Letters in Applied Microbiology

Microbes in the news

Bacteria discovered by scientists in London cuts dependence on commercial fertilizers – John Miner – LFPress

Fungus makes tree frogs sing – Nature

Michigan researchers start $9.2M effort to study bacteria – Click on Detroit

“Nightmare Bacteria” Found in Southern California Sewage Treatment Plants – Alexander Haro – The Inertia

Two Starbucks Items Voluntarily Recalled Due to Bacteria, Allergen Risk – Gillian Mohney – ABC News

Science, publishing, and career

Scientific record: Class uncorrected errors as misconduct – Sophien Kamoun – Nature

A Multi-dimensional Investigation of the Effects of Publication Retraction on Scholarly Impact – Xin Shuai – Arxiv

[hr]

Somewhere between March 8 and March 9, 2016

Posted on by

Human symbionts inject to persist, diet and exercise in mice, a 17-year long experiment, and using peanut butter as a vehicle to deliver probiotics in developing countries.

Human skin microbiome

Proteobacteria from the human skin microbiota: Species-level diversity and hypotheses – C. Cosseau – One Health

Human respiratory microbiome

Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia –  Etienne Ruppé – Future Microbiology

Human gut microbiome

Analysis of Gut Microbiota in Coronary Artery Disease Patients: a Possible Link between Gut Microbiota and Coronary Artery Disease – Takuo Emoto – Journal of Atherosclerosis and Thrombosis

PhD Thesis: Indigenous Australians have a distinctive gut microbial profile compared to Caucasian controls and patients with inflammatory bowel disease – Iyngkaran, Guruparan – Melbourne Medical School

Review: Changes in the Intestinal Microbiome and Alcoholic- and Non-alcoholic Liver Diseases—Causes or Effects? – Naga S. Betrapally – Gastroenterology

Review: Microbiome alterations in HIV infection a review – B Williams – Cellular Microbiology

Review: Extensive Intestinal Resection Triggers Behavioral Adaptation, Intestinal Remodeling and Microbiota Transition in Short Bowel Syndrome – Camille Mayeur – MDPI Microorganisms

Microbiome models

Human symbionts inject and neutralize antibacterial toxins to persist in the gut – Aaron G. Wexler – PNAS

The Effect of Diet and Exercise on Intestinal Integrity and Microbial Diversity in Mice – Sara C. Campbell – PLOS ONE

Chronic Psychological Stress Disrupted the Composition of the Murine Colonic Microbiota and Accelerated a Murine Model of Inflammatory Bowel Disease – Yohei Watanabe – PLOS ONE

Flavanol-Enriched Cocoa Powder Alters the Intestinal Microbiota, Tissue and Fluid Metabolite Profiles, and Intestinal Gene Expression in Pigs – Saebyeol Jang – The Journal of Nutrition

Deletion of the Toll-Like Receptor 5 Gene Per Se Does Not Determine the Gut Microbiome Profile That Induces Metabolic Syndrome: Environment Drumpfs Genotype
Wei Zhang – PLOS ONE

Animal microbiome

The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance – Bettina Glasl – ISME Journal

Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis – Filip Husnik – BioRxiv

No access for me, but I assume this is in birds: Microbial shifts associated with necrotic enteritis – Gunther Antonissen – Avian Pathology

Plant, root, and soil microbiome
Orchids: Differences in mycorrhizal communities between Epipactis palustris, E. helleborine and its presumed sister species E. neerlandica – Hans Jacquemyn – Annals of Botany

Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment – Ben Bond-Lamberty – PLOS ONE

Evaluation of a diagnostic microarray for the detection of major bacterial pathogens of potato from tuber samples – Y. Degefu – EPPO Bulletin

Shifts in symbiotic associations in plants capable of forming multiple root symbioses across a long-term soil chronosequence – Felipe E. Albornoz – Ecology and Evolution

Bacterial diversity and community along the succession of biological soil crusts in the Gurbantunggut Desert, Northern China – Bingchang Zhang – Journal of Basic Microbiology

Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest – Zhenping Yang – PLOS ONE

Characterization of bacterial communities in lithobionts and soil niches from Victoria Valley, Antarctica – Marc W. Van Goethem – FEMS Microbiology Ecology

Bacterial indicator taxa in soils under different long-term agricultural management – N.G. Jiménez-Bueno – Journal of Applied Microbiology

Water and extremophile microbiome

Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge – Huiluo Cao – Scientific Reports

Nutrient treatments alter microbial mat colonization in two glacial meltwater streams from the McMurdo Dry Valleys, Antarctica – Tyler J. Kohler – FEMS Microbiology Ecology

Bioreactor microbiology

Gut microbiota-involved mechanisms in enhancing systemic exposure of ginsenosides by coexisting polysaccharides in ginseng decoction – Shan-Shan Zhou – Scientific Reports

Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis
Gang Luo – Biotechnology for Biofuels

Waste and pollution microbiology

Temporal dynamics of biotic and abiotic drivers of litter decomposition – Pablo García-Palacios – Ecology Letters

Microbial Community Structures in Petroleum Contaminated Soils at an Oil Field, Hebei, China – Yizhi Sheng – CLEAN – Soil, Air, Water

Effect of microbial community structure on organic removal and biofouling in membrane adsorption bioreactor used in seawater pretreatment – Sanghyun Jeong – Chemical Engineering Journal

Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems – Journal of Environmental Sciences – A.O. Babatunde

Functional foods and food microbiology

For applications in developing countries: Influence of probiotics, included in peanut butter, on the fate of selected Salmonella and Listeria strains under simulated gastrointestinal conditions – Y.A.K. Klu – Journal of Applied Microbiology

Bioinformatics and metagenomics

Read networks and k-laminar graphs – Finn Volkel – ArXiv

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment – Jeongsu Oh – PLOS ONE

Protocol: Using QIIME to Evaluate the Microbial Communities Within Hydrocarbon Environments – Luke K. Ursell – Springer Protocols Handbooks

Regression Analysis for Microbiome Compositional Data – Pixu Shi – ArXiv

bioOTU: An Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences – Chen Shi-Yi – Journal of Computational Biology

Techniques

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies – James L. O’Donnell – PLOS ONE

More microbiology

Alice’s living croquet theory – Didier Raoult – International Journal of Antimicrobial Agents

Genomic approaches for understanding dengue: insights from the virus, vector, and host – Shuzhen Sim – Genome Biology

Microbes and infection

Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using a high-density resequencing pathogen microarray platform – Moussa Kourout – Transfusion

Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages – Rachelle Mariano – mSystems

Microbes in the news

Cutting Board Companions – Katherine Dahlhausen – MicroBEnet @PhDKD

Standard practice of giving premature babies antibiotics needs to be rethought, argues new study – Jessica Firger – Newsweek

Bacterial brawls mark life in the gut’s microbiome – Bill Hathaway – Phys.org

How your microbiome can put you at the scene of the crime – Kai Kupferschmidt – Science

Soy protein may diversify gut microbiota more than dairy protein: Study – Stephen Daniells – Nutraingredients
Sleep Deprivation Caused By Jet Lag And Shift Work Could Be Treated Through Your Gut Microbiome – Cayla Dengate – Huffington Post

U-M Students Analyze Their Own Biological Samples to Study How Microbes Affect Human Health – Infection Control Today

#1 is outdated but rest ok: 10 things you need to know about your gut – Naomi Mead – Netdoctor

The Dannon Company Announces Fourth-Annual Winner of Yogurt and Probiotics Fellowship Grant: Micah Eimerbrink – BusinessWire

Science, publishing, and career

Insights into the PeerJ Preprint: “Gender bias in open source” – PeerJ Blog

Bik’s Picks

I Speak Whale: Vast assembly of vocal marine mammals from diverse species on fish spawning ground – Delin Wang – Nature

[hr]

March 5, 2016

Posted on by

Lung microbes in Cystic Fibrosis, microbiota of reindeer, strawberry phyllosphere, and microbes in raindust.

Pregnancy and birth

Dynamics of Gut Microbiota According to the Delivery Mode in Healthy Korean Infants – Eun Lee- Allergy Asthma Immunol Res.

Review: Respiratory Microbiome of New-Born Infants – David J. Gallacher – Frontiers in Pediatrics

Review: Bosom Buddies: The Symbiotic Relationship Between Infants and Bifidobacterium longum ssp. longum and ssp. infantis. Genetic and Probiotic Features – Silvia Arboleya – Annual Review of Food Science and Technology

Review: Maternal microbiome – A pathway to preterm birth – Angela E. Vinturache – Seminars in Fetal and Neonatal Medicine

Human respiratory microbiome

Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease – Deborah A. Hogan – PLOS ONE

Human oral microbiome

Levels of Candidate Periodontal Pathogens in Subgingival Biofilm – R.R.D.S Oliveira – Journal of Dental Research

Human gut microbiome

Effects of plant stanol ester consumption on fasting plasma oxy(phyto)sterol concentrations as related to fecal microbiota characteristics – Sabine Baumgartner – The Journal of Steroid Biochemistry and Molecular Biology

Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients – Forbes, Jessica D. – Inflammatory Bowel Diseases

Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis – Ohad Manor – Scientific Reports

Research highlight: Growth impairment in undernourished children – Claire Greenhill – Nature Reviews Endocrinology

Review: Elucidating the role of the host genome in shaping microbiome composition – Emily R. Davenport – Gut Microbes

Review: The Microbiome: A Key Regulator of Stress and Neuroinflammation – Kieran Rea – Neurobiology of Stress

Review: The Brain-Gut-Microbiome Axis: What Role Does it Play in Autism Spectrum Disorder? – Ruth Ann Luna – Current Developmental Disorders Reports

Review: Microbes and the Mind: Emerging Hallmarks of the Gut Microbiota-Brain Axis – Kylynda C. Bauer – Cellular Microbiology

Review: The human gut microbiome and its dysfunctions through the meta-omics prism – Stanislas Mondot – Annals of the New York Academy of Sciences

Animal models

Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model – Gaorui Bian – Environmental Microbiology

Effects of environmental temperature on the gut microbial communities of tadpoles – Kevin D. Kohl – Environmental Microbiology

Apple-Derived Pectin Modulates Gut Microbiota, Improves Gut Barrier Function, and Attenuates Metabolic Endotoxemia in Rats with Diet-Induced Obesity – Tingting Jiang – MDPI Nutrients

The effects of fecal microbial transplantation on microbiome and immunity in SIV-infected macaques – Tiffany Hensley-McBain – Journal of Virology

Soy Protein Compared with Milk Protein in a Western Diet Increases Gut Microbial Diversity and Reduces Serum Lipids in Golden Syrian Hamsters – Dustie N Butteiger – Journal of Nutrition

Review: The interplay between intestinal bacteria and host metabolism in health and disease: lessons from Drosophila melanogaster – Adam C. N. Wong – Disease Models & Mechanisms

Animal microbiome

New Insights into the Microbiota of the Svalbard Reindeer Rangifer tarandus platyrhynchus – Sylwia Zielińska – Frontiers in Microbiology

Geographically conserved microbiomes of four temperate water tunicates – Patrick L. Cahill – Environmental Microbiology Reports

Twenty five new viruses associated with the Drosophilidae (Diptera) – Claire L Webster – bioRxiv

Plant, root, and soil microbiome

Soil Microbial Community Interactions Under Tillage Systems in Australia – Vivian A. Rincon-Florez – Plant, Soil and Microbes

Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest – Zhenping Yang – PLOS ONE

Dispersal of Bacillus subtilis and its effect on strawberry phyllosphere microbiota under open field and protection conditions – Feng Wei – Scientific Reports

Temporally Variable Geographical Distance Effects Contribute to the Assembly of Root-Associated Fungal Communities – Christopher J. Barnes – Frontiers in Microbiology

Elevation gradient of soil bacterial communities in bamboo plantations – Yu-Te Lin – Botanical Studies

Soil microbial functional capacity and diversity in a millet-shrub intercropping system of semi-arid Senegal – S. Diakhaté – Journal of Arid Environments

Bioaugmentation of microbes to restore coastal wetland plants to protect land from coastal erosion – Regina Bledsoe – International Biodeterioration & Biodegradation

Review: Nutrient scavenging activity and antagonistic factors of non-photobiont lichen-associated bacteria: a review – M. Auður Sigurbjörnsdóttir – World Journal of Microbiology and Biotechnology

Water, rain, and extremophile microbiome

Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin – Silke Langenheder – Environmental Microbiology Reports

Comparative summer dynamics of surface cyanobacterial communities in two connected lakes from the west of Ireland – N. Touzet – Science of The Total Environment

Dust Rains Deliver Diverse Assemblages of Microorganisms to the Eastern Mediterranean – Ghida Nouhad Itani – Scientific Reports

Protistan diversity and activity inferred from RNA and DNA at a coastal ocean site in the eastern North Pacific – Sarah K. Hu – FEMS Microbiology Ecology

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge – Julie L. Meyer – Scientific Reports

Biodigester microbiology

This one sounded wrong: Microbial diversity in an anaerobic digester with biogeographical proximity to geothermal active region – Rishi Mahajan – Environmental Technology

Food microbiology

Impact of mulches and growing season on indicator bacteria survival during lettuce cultivation – Aixia Xu – International Journal of Food Microbiology

Built environment microbiology

Seasonal Dynamics of the Airborne Bacterial Community and Selected Viruses in a Children’s Daycare Center – Aaron J. Prussin II – PLOS ONE

Bioweathering Potential of Cultivable Fungi Associated with Semi-Arid Surface Microhabitats of Mayan Buildings – Benjamín O. Ortega-Morales – Frontiers in Microbiology

Microbiome of death

Review: The Thanatomicrobiome: A Missing Piece of the Microbial Puzzle of Death – Gulnaz T. Javan – Frontiers in Microbiology

Waste and pollution microbiology

Isolation and characterization of yeasts associated with plants growing in heavy-metal- and arsenic-contaminated soils – Juan Ramos-Garza – Canadian Journal of Microbiology

Review: Understanding the development of environmental resistance among microbes: A Review – Jatin Srivastava – CLEAN – Soil, Air, Water

Review: Microbial communities, processes and functions in acid mine drainage ecosystems – Lin-xing Chen – Current Opinion in Biotechnology

Infection microbiology

Absence of Serological Evidence of Rickettsia spp., Bartonella spp., Ehrlichia spp. and Coxiella burnetii Infections in American Samoa – Colleen Lau – Ticks and Tick-borne Diseases

Comparison between a Broad-Range Real-Time and a Broad-Range End-Point PCR Assays for the Detection of Bacterial 16S rRNA in Clinical Samples – Mariam Meddeb – Annals of Clinical & Laboratory Science

Metagenomics and bioinformatics

Capturing the most wanted taxa through cross-sample correlations – Mathieu Almeida – The ISME Journal

MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation
Gabriele Andrea Lugli – FEMS Microbiology Letters

Sequence techniques

Microbial Ecology in the Era of Next Generation Sequencing – Surajit De Mandal – Omics: Next Generation: Sequencing & Applications

Microbial Ecology

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes? – Emily B. Graham – Frontiers in Microbiology

Microbes in the news

Would you try to vaginally “seed” your baby’s microbiome after a C-section – Jonathan Eisen – The Tree of Life

Science, publishing, and career

This Paper Should Not Have Been Retracted: #HandofGod highlights the worst aspects of science twitter – Andrew David Thaler – Southern Friend Science

The “Creator” paper, Post-pub Peer Review, and Racism Among Scientists – Dr24hours – Complex Roots

UC reclassifies master’s degrees, charges elevated tuition – Nanette Asimov – SF Chronicle

She Wanted to Do Her Research. He Wanted to Talk ‘Feelings.’ – A. Hope Jahren – NY Times

[hr]

March 4, 2015

Posted on by

Long term use of protein pump inhibitors, bovine genetics and microbial methane, fungi for biodegradation, Bayesian fingerprinting.

Human oral microbiome

Impact of smoking on experimental gingivitis. A clinical, microbiological and immunological prospective study – D. C. Peruzzo – Journal of Periodontal Research

Human gut microbiome

A comparison of the gut microbiome between long-term users and non-users of proton pump inhibitors – A. G. Clooney – Alimentary Pharmacology & Therapeutics

Animal microbiome

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance – Rainer Roehe – PLOS Genetics

When Parasites Are Good for Health: Cestode Parasitism Increases Resistance to Arsenic in Brine Shrimps – Marta I. Sánchez – PLOS Pathogens

Plant, root, and soil microbiome

A New Perspective on Sustainable Soil Remediation—Case Study Suggests Novel Fungal Genera Could Facilitate in situ Biodegradation of Hazardous Contaminants – Lauren M. Czaplicki – Remediation Journal

Fungal effects on plant–plant interactions contribute to grassland plant abundances: evidence from the field – Jonathan A. Bennett – Journal of Ecology

Status of microbial diversity in agroforestry systems in Tamil Nadu, India – Srinivasan Radhakrishnan – Journal of Basic Microbiology

Water microbiome

Microfungi Potentially Pathogenic for Humans Reported in Surface Waters Utilized for Recreation – Anna Biedunkiewicz – CLEAN – Soil, Air, Water

Waste and pollution microbiology

Bait and scrape: An approach for assessing biofilm microbial communities on organic media used for gas-phase biofiltration – Jason P. Oliver – Ecological Engineering

Food microbiology

Review: Microbial Safety of Wood in Contact with Food: A Review – Florence Aviat – Comprehensive Reviews in Food Science and Food Safety

Bioinformatics

Species Identification by Bayesian Fingerprinting: A Powerful Alternative to DNA Barcoding – Ziheng Yang – BioRxiv

blastjs: a BLAST+ wrapper for Node.js – Martin Page – BMC Research Notes

Microbes in the news

uBiome Investigates Health Implications of Seniors’ Changing Microbiomes, Seeks Participants – Benzinga

Mystery bacteria linked to 18 deaths in Wisconsin – CBS News

Includes Pat Schloss: 78 Fellows Elected to the American Academy of Microbiology – ASM

Science, publishing, and career

A Science Journal Invokes ‘the Creator,’ and Science Pushes Back – Madison Kotack – Wired

PLOS ONE retracting paper that cites “the Creator” – Alison McCook – Retraction Watch

#IAmAResearchParasite – Marcia McNutt – Science

Making a game of science – Elizabeth Pennisi – Science

Yes, Even CRISPR Pioneer Jennifer Doudna Experiences Gender Bias – Lisa Potter and Jon Brooks – KQED

[hr]

March 3, 2016

Posted on by

Gut microbiome of Indian Nicobarese tribe, CDI patients’ stories about life before and after stool transplants, cryptic species in Nematoda, and similar fungi at opposite poles.

Pregnancy and birth

Review: The Developing Microbiome of the Preterm Infant – Mara E. DiBartolomeo – Clinical Therapeutics

Gut colonization by aerobic microorganisms is associated with route and type of nutrition in premature neonates – Ülle Parm – Nutrition Research

Human oral microbiome

Influence of a triclosan toothpaste on periodontopathic bacteria and periodontitis progression in cardiovascular patients: a randomized controlled trial – G. J. Seymour – Journal of Periodontal Research

Human respiratory microbiome

Review: Microbes and asthma: Opportunities for intervention – Hermelijn H. Smits – Journal of Allergy and Clinical Immunology

Understanding Persistent Bacterial Lung Infections: Clinical Implications Informed by the Biology of the Microbiota and Biofilms – Alexa A. Pragman – Clinical Pulmonary Medicine

Human gut microbiome

Elucidating the richness of bacterial groups in the gut of nicobarese tribal community – Perspective on their lifestyle transition – Maile Anwesh – Anaerobe

Resistant potato starches (type 4 RS) exhibit varying effects on laxation with and without phylum level changes in microbiota: A randomised trial in young adults – W.J. Dahl – Journal of Functional Foods

Recommended: Fecal microbiota transplantation for recurrent Clostridium difficile infection: The patient experience – Amy L. Pakyz – American Journal of Infection Control

Analysis of Gut Microbiome Reveals Significant Differences Between Men with Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls – Daniel A. Shoskes – The Journal of Urology

RiMINI – the influence of rifaximin on minimal hepatic encephalopathy (MHE) and on the intestinal microbiome in patients with liver cirrhosis: study protocol for a randomized controlled trial – Christian Schulz – BMC Trials

Editorial: Dysbiosis in fungal microbiota in IBD – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Models of microbiome research

Functional characterization of inflammatory bowel disease-associated gut dysbiosis in gnotobiotic mice – Hiroko Nagao-Kitamoto – CMGH Cellular and Molecular Gastroenterology and Hepatology

Effect of breast feeding time on physiological, immunological and microbial parameters of weaned piglets in an intensive breeding farm – G.R. García – Veterinary Immunology and Immunopathology

Animal microbiome

Prevalence of potential nitrogen-fixing, green sulfur bacteria in the skeleton of reef-building coral Isopora palifera – Shan-Hua Yang – Limnology and Oceanography

An investigation of the microbiota in uterine flush samples and endometrial biopsies from dairy cows during the first 7 weeks postpartum – Lif Rødtness Vesterby Knudsen – Theriogenology

Coexisting cryptic species of the Litoditis marina complex (Nematoda) show differential resource use and have distinct microbiomes with high intraspecific variability – S Derycke – Molecular Ecology

Hologenome analysis of two marine sponges with different microbiomes – Taewoo Ryu – BMC Genomics

Plant, root, and soil microbiome

Land use change in the Amazon rainforest favors generalist fungi – Rebecca C Mueller – Functional Ecology

Drivers of phosphorus limitation across soil microbial communities – Petr Čapek – Functional Ecology

Effects of changes in straw chemical properties and alkaline soils on bacterial communities engaged in straw decomposition at different temperatures – Guixiang Zhou – Scientific Reports

Soil pH is a Key Determinant of Soil Fungal Community Composition in the Ny-Ålesund Region, Svalbard (High Arctic) – Tao Zhang – Frontiers in Microbiology

Diversity of endophytic fungal and bacterial communities in Ilex paraguariensis grown under field conditions – María Laura Pérez – World Journal of Microbiology and Biotechnology

Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches – Steven D. Leavitt – Scientific Reports

Rhizosphere competence of wild-type and genetically-engineered Pseudomonas brassicacearum is affected by the crop species – Stacey Blouin Bankhead – Phytopathology

Actinorhizal Alder Phytostabilization Alters Microbial Community Dynamics in Gold Mine Waste Rock from Northern Quebec: A Greenhouse Study – Katrina L. Callender – PLOS ONE

Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs – A. Ö. C. Dupont – Environmental Microbiology

Water and extremophile microbiome

Diazotroph community structure in the deep oxygen minimum zone of the Costa Rica Dome – Shunyan Cheung – Journal of Plankton Research

Not poles apart: Antarctic soil fungal communities show similarities to those of the distant Arctic – Filipa Cox – Ecology Letters

Food microbiology

Salmonella in Shell Eggs: Mechanisms, Prevention and Detection – Seockmo K – Omics Journal of Nutrition & Food Sciences

Intensive aquaculture selects for increased virulence and interference competition in bacteria – Lotta-Riina Sundberg – Proceedings of the Royal Society B

Application of electrolyzed oxidizing water in production of radish sprouts to reduce natural microbiota – Chunling Zhang – Food Control

Biodiversity of culturable psychrotrophic microbiota in raw milk attributable to refrigeration conditions, seasonality and their spoilage potential – Nuwan R. Vithanage – International Dairy Journal

Microbiological characteristics of fresh tofu produced in small industrial scale and identification of specific spoiling microorganisms (SSO) – Franca Rossi – LWT – Food Science and Technology

Built Environment and Waste Microbiome

The efficacy of disinfectants in the decontamination of dental unit water lines: an in vitro laboratory study – Mrudula Patel – BDJ Open

Review: Bacterial communities in full-scale wastewater treatment systems – Agnieszka Cydzik-Kwiatkowska – World Journal of Microbiology and Biotechnology

Preferential methanogenic biodegradation of short-chain n-alkanes by microbial communities from two different oil sands tailings ponds – Mohd Faidz Mohamad Shahimin – Science of The Total Environment

Microbes in space

Two older papers that showed up in my PubMed alert today:
Review: The Significance of Microbe-Mineral-Biomarker Interactions in the Detection of Life on Mars and Beyond – Wilfred F.M. Röling – Astrobiology
Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions – Andrew C. Schuerger – Astrobiology

Phages and viruses

Diversity of phage infection types and associated terminology: the problem with “Lytic or Lysogenic” – Zack Hobbs – FEMS Microbiology Letters

Techniques

Effect of Freezing Conditions on Fecal Bacterial Composition in Pigs – Barbara U. Metzler-Zebeli – MDPI Animals

Microbes in the news

Astronaut Scott Kelly back on earth, Northwestern profs celebrate – Chicago Sun Times

Microbial Manifesto: The Global Push to Understand the Microbiome (Kavli Roundtable) – Alan Brown – Live Science

‘Gut’ bacteria may help put a kink in family obesity cycle – Science Codex

[hr]

March 2, 2016

Posted on by

Metagenomics of weight loss, and the microbiomes of pollen, offices, and Irish Lough Neagh.

Human respiratory microbiome

Alterations of the Nasopharyngeal Microbiota in Infants with Cystic Fibrosis. Cystic Fibrosis Transmembrane Conductance Regulator and Antibiotic Effects – Edith T. Zemanick – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing – Sandrine Louis – PLOS ONE

Influence of the Biliary System on Biliary Bacteria Revealed by Bacterial Communities of the Human Biliary and Upper Digestive Tracts – Fuqiang Ye – PLOS ONE

Animal microbiome

Horizontal gene transfer from bacteria has enabled the plant-parasitic nematode Globodera pallida to feed on host-derived sucrose – Etienne G.J. Danchin – Molecular Biology and Evolution

Review: The interplay between intestinal bacteria and host metabolism in health and disease: lessons from Drosophila melanogaster – Adam C. N. Wong – Disease Models & Mechanisms

Plant, root, and soil microbiome

Pollen-Associated Microbiome Correlates with Pollution Parameters and the Allergenicity of Pollen – Andrea Obersteiner – PLOS ONE

Built environment microbiome

Geography and location are the primary drivers of office microbiome composition – John Chase – PeerJ Preprint

Water microbiome

Commentary: Is El Niño a long-distance corridor for waterborne disease? – Jaime Martinez-Urtaza – Nature Microbiology

Viruses

Viruses’ origin could relate to the act of prey among primitive life forms during the old ages – Eslam Abbas – PeerJ Preprint

Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland – Timofey Skvortsov – PLOS ONE

Microbial ecology

The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography – Marguerite Lapierre – Molecular Biology and Evolution

Social amoebae trap and kill bacteria by casting DNA nets – Xuezhi Zhang – Nature Communications

Bioinformatics

LS3: A method for improving phylogenomic inferences when evolutionary rates are heterogeneous among taxa – Carlos J. Rivera-Rivera – Molecular Biology and Evolution

Microbes in the news

Bacteria or virus? New tests may identify what’s causing your infection – Fox News

El Niño Opens Up a Bridge for Bacteria to Travel Between Continents – Esther Inglis-Arkell – Gizmodo

Building Off NYC Subway Study, Consortium to Profile Metagenomes of Transit Systems in 45 Cities – Monica Heger – GenomeWeb

White House calls for microbiome science support – Stephen Daniells – Nutraingredients[hr]